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At least 235 records · Page 13

Operator-level quantum acceleration of non-logconcave sampling

Sampling from probability distributions of the form 𝝈 ∝ e −𝜷V , where V is a continuous potential, is a fundamental task across physics, chemistry, biology, computer science, and statistics. However, when V is nonconvex, the resulting distribution becomes non-logconcave, and classical methods such as Langevin dynamics often exhibit poor performance. We introduce a quantum algorithm that provably accelerates a broad class of continuous-time sampling dynamics. For Langevin dynamics, our method encodes the target Gibbs measure into the amplitudes of aquantum state, identified as the kernel of a block matrix derived from a factorization of the Witten Laplacian operator. This connection enables Gibbs sampling via singular value thresholding and yields up to a quartic quantum speedup over best-knownclassical Langevin-based methods in the non-logconcave setting. Building on this framework, we further develop the first quantum algorithm that accelerates replica exchange Langevin diffusion, a widely used method for sampling from complex, rugged energy landscapes.

97 MATHEMATICS AND COMPUTING↗

Towards long-term standardised carbon and greenhouse gas observations for monitoring Europe’s terrestrial ecosystems: A review

Research infrastructures play a key role in launching a new generation of integrated long-term, geographically distributed observation programmes designed to monitor climate change, better understand its impacts on global ecosystems, and evaluate possible mitigation and adaptation strategies. The pan-European Integrated Carbon Observation System combines carbon and greenhouse gas (GHG; CO 2 , CH 4 , N 2 O, H 2 O) observations within the atmosphere, terrestrial ecosystems and oceans. High-precision measurements are obtained using standardised methodologies, are centrally processed and openly available in a traceable and verifiable fashion in combination with detailed metadata. The Integrated Carbon Observation System ecosystem station network aims to sample climate and land-cover variability across Europe. In addition to GHG flux measurements, a large set of complementary data (including management practices, vegetation and soil characteristics) is collected to support the interpretation, spatial upscaling and modelling of observed ecosystem carbon and GHG dynamics. The applied sampling design was developed and formulated in protocols by the scientific community, representing a trade-off between an ideal dataset and practical feasibility. Finally, the use of open-access, high-quality and multi-level data products by different user communities is crucial for the Integrated Carbon Observation System in order to achieve its scientific potential and societal value.

54 ENVIRONMENTAL SCIENCES↗

Extraction and isotopic analysis of medium molecular weight hydrocarbons from Murchison using supercritical carbon dioxide

The large variety of organic compounds present in carbonaceous chondrites poses particular problems in their analysis not the least of which is terrestrial contamination. Conventional analytical approaches employ simple chromatographic techniques to fractionate the extractable compounds into broad classes of similar chemical structure. However, the use of organic solvents and their subsequent removal by evaporation results in the depletion or loss of semi-volatile compounds as well as requiring considerable preparative work to assure solvent purity. Supercritical fluids have been shown to provide a powerful alternative to conventional liquid organic solvents used for analytical extractions. A sample of Murchison from the Field Museum was analyzed. Two interior fragments were used; the first (2.85 g) was crushed in an agate pestel and mortar to a grain size of ca. 50-100 micron, the second (1.80 g) was broken into chips 3-8 mm in size. Each sample was loaded into a stainless steel bomb and placed in the extraction chamber of an Isco supercritical fluid extractor maintained at 35 C. High purity (99.9995 percent) carbon dioxide was used and was pressurized using an Isco syringe pump. The samples were extracted dynamically by flowing CO2 under pressure through the bomb and venting via a 50 micron fused filica capillary into 5 mls of hexane used as a collection solvent. The hexane was maintained at a temperature of 0.5 C. A series of extractions were done on each sample using CO2 of increasing density. The principal components extracted in each fraction are summarized.

Gilmour, Iain↗

High-throughput quantification of quasistatic, dynamic and spall strength of materials across 10 orders of strain rates

Abstract The response of metals and their microstructures under extreme dynamic conditions can be markedly different from that under quasistatic conditions. Traditionally, high strain rates and shock stresses are achieved using cumbersome and expensive methods such as the Kolsky bar or large spall experiments. These methods are low throughput and do not facilitate high-fidelity microstructure–property linkages. In this work, we combine two powerful small-scale testing methods, custom nanoindentation, and laser-driven microflyer (LDMF) shock, to measure the dynamic and spall strength of metals. The nanoindentation system is configured to test samples from quasistatic to dynamic strain-rate regimes. The LDMF shock system can test samples through impact loading, triggering spall failure. The model material used for testing is magnesium alloys, which are lightweight, possess high-specific strengths, and have historically been challenging to design and strengthen due to their mechanical anisotropy. We adopt two distinct microstructures, solutionized (no precipitates) and peak-aged (with precipitates) to demonstrate interesting upticks in strain-rate sensitivity and evolution of dynamic strength. At high shock-loading rates, we unravel an interesting paradigm where the spall strength vs. strain rate of these materials converges, but the failure mechanisms are markedly different. Peak aging, considered to be a standard method to strengthen metallic alloys, causes catastrophic failure, faring much worse than solutionized alloys. Our high-throughput testing framework not only quantifies strength but also teases out unexplored failure mechanisms at extreme strain rates, providing valuable insights for the rapid design and improvement of materials for extreme environments.

Eswarappa Prameela, Suhas (ORCID:0000000334530184)↗

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase

Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvents, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness toward designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an x-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an x-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. In addition, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.

Chemistry↗

Convergent properties of vestibular-related brain stem neurons in the gerbil

Three classes of vestibular-related neurons were found in and near the prepositus and medial vestibular nuclei of alert or decerebrate gerbils, those responding to: horizontal translational motion, horizontal head rotation, or both. Their distribution ratios were 1:2:2, respectively. Many cells responsive to translational motion exhibited spatiotemporal characteristics with both response gain and phase varying as a function of the stimulus vector angle. Rotationally sensitive neurons were distributed as Type I, II, or III responses (sensitive to ipsilateral, contralateral, or both directions, respectively) in the ratios of 4:6:1. Four tested factors shaped the response dynamics of the sampled neurons: canal-otolith convergence, oculomotor-related activity, rotational Type (I or II), and the phase of the maximum response. Type I nonconvergent cells displayed increasing gains with increasing rotational stimulus frequency (0.1-2.0 Hz, 60 degrees /s), whereas Type II neurons with convergent inputs had response gains that markedly decreased with increasing translational stimulus frequency (0.25-2.0 Hz, +/-0.1 g). Type I convergent and Type II nonconvergent neurons exhibited essentially flat gains across the stimulus frequency range. Oculomotor-related activity was noted in 30% of the cells across all functional types, appearing as burst/pause discharge patterns related to the fast phase of nystagmus during head rotation. Oculomotor-related activity was correlated with enhanced dynamic range compared with the same category that had no oculomotor-related response. Finally, responses that were in-phase with head velocity during rotation exhibited greater gains with stimulus frequency increments than neurons with out-of-phase responses. In contrast, for translational motion, neurons out of phase with head acceleration exhibited low-pass characteristics, whereas in-phase neurons did not. Data from decerebrate preparations revealed that although similar response types could be detected, the sampled cells generally had lower background discharge rates, on average one-third lower response gains, and convergent properties that differed from those found in the alert animals. On the basis of the dynamic response of identified cell types, we propose a pair of models in which inhibitory input from vestibular-related neurons converges on oculomotor neurons with excitatory inputs from the vestibular nuclei. Simple signal convergence and combinations of different types of vestibular labyrinth information can enrich the dynamic characteristics of the rotational and translational vestibuloocular responses.

Non-NASA Center↗

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4

As the application of computational methods in drug discovery pipelines becomes more widespread it is increasingly important to understand how reproducible their results are and how sensitive they are to choices made in simulation setup and analysis. Here we use ensemble simulation protocols, termed ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent), to investigate the sensitivity of the popular molecular mechanics Poisson-Boltzmann surface area (MMPBSA) methodology. Using the bromodomain-containing protein 4 (BRD4) system bound to a diverse set of ligands as our target, we show that robust rankings can be produced only through combining ensemble sampling with multiple trajectories and enhanced solvation via an explicit ligand hydration shell.

59 BASIC BIOLOGICAL SCIENCES↗

The dynamical state of eROSITA clusters and its impact on the brightest cluster galaxy luminosity

The first Spectrum-Roentgen-Gamma (SRG) eROSITA public release contains 12 247 clusters and groups from its first 6 months of operation. We used the offset between the brightest cluster galaxy (BCG) and the X-ray peak ( D BCG − X ) to classify the cluster dynamical state of 3946 galaxy clusters and groups. We aim to investigate the evolution of the merger and relaxed cluster distributions with redshift and mass, and the distributions’ impact on the BCG. We used the X-ray peak from the eROSITA survey and the BCG position from the LS DR10 optical data, which includes the DECam eROSITA Survey optical data, to measure the D BCG − X offset. We modelled the distribution of D BCG − X , in units of R 500 , as the sum of two Rayleigh distributions representing the cluster’s relaxed and disturbed populations, and explored their evolution with redshift and mass. To explore the impact of the cluster’s dynamical state on the BCG luminosity, we separated the main sample according to the dynamical state. We defined clusters as relaxed if D BCG − X < 0.25R500, disturbed if D BCG − X > 0.5R500, and ‘diverse’ if 0.25R500 < D BCG − X < 0.5R500. We find no evolution of the merging fraction with redshift or mass. The width of the relaxed distribution increases with redshift, while the width of the two Rayleigh distributions decreases with mass. The analysis reveals that BCGs in relaxed clusters are brighter than BCGs in both the disturbed and diverse cluster populations. The most significant differences are found for high-mass clusters at higher redshifts. The results suggest that BCGs in low-mass clusters are less centrally bound than those in high-mass systems, irrespective of the dynamical state. Over time, BCGs in relaxed clusters progressively align with the potential centre. This alignment correlates with their luminosity growth relative to BCGs in dynamically disturbed clusters, underscoring the critical role of the cluster’s dynamical state in regulating BCG evolution.

galaxy clusters↗

Visible emission spectra of thermographic phosphors under x-ray excitation

Thermographic phosphors have been employed for temperature sensing in challenging environments, such as on surfaces or within solid samples exposed to dynamic heating, because of the high temporal and spatial resolution that can be achieved using this approach. Typically, UV light sources are employed to induce temperature-sensitive spectral responses from the phosphors. However, it would be beneficial to explore x-rays as an alternate excitation source to facilitate simultaneous x-ray imaging of material deformation and temperature of heated samples and to reduce UV absorption within solid samples being investigated. Here, the phosphors BaMgAl 10 O 17 :Eu (BAM), Y 2 SiO 5 :Ce, YAG:Dy, La 2 O 2 S:Eu, ZnGa 2 O 4 :Mn, Mg 3 F 2 GeO 4 :Mn, Gd 2 O 2 S:Tb, and ZnO were excited using incident synchrotron x-ray radiation. These materials were chosen to include conventional thermographic phosphors as well as x-ray scintillators (with crossover between these two categories). X-ray-induced thermographic behavior was explored through the measurement of visible spectral response with varying temperature. The incident x-rays were observed to excite the same electronic energy level transitions in these phosphors as UV excitation. Similar shifts in the spectral response of BAM, Y 2 SiO 5 :Ce, YAG:Dy, La 2 O 2 S:Eu, ZnGa 2 O 4 :Mn, Mg 3 F 2 GeO 4 :Mn, and Gd 2 O 2 S:Tb were observed when compared to their response to UV excitation found in literature. Some phosphors were observed to thermally quench in the temperature ranges tested here, while the response from others did not rise above background noise levels. This may be attributed to the increased probability of non-radiative energy release from these phosphors due to the high energy of the incident x-rays. These results indicate that x-rays can serve as a viable excitation source for phosphor thermometry.

42 ENGINEERING↗

A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited

Because lipid bilayers can bend and stretch in ways similar to thin elastic sheets, physical models of bilayer deformation have utilized mechanical constants such as the moduli for bending rigidity (κ C ) and area compressibility (K A ). However, the use of these models to quantify the energetics of membrane deformation associated with protein-membrane interactions, and the membrane response to stress is often hampered by the shortage of experimental data suitable for the estimation of the mechanical constants of various lipid mixtures. Although computational tools such as molecular dynamics simulations can provide alternative means to estimate K A values, current approaches suffer significant technical limitations. Here, in this study, we present a novel, to our knowledge, computational framework that allows for a direct estimation of K A values for individual bilayer leaflets. The theory is based on the concept of elasticity and derives K A from real-space analysis of local thickness fluctuations sampled in molecular dynamics simulations. We explore and validate the model on a large set of single and multicomponent bilayers of different lipid compositions and sizes, simulated at different temperatures. The calculated bilayer compressibility moduli agree with values estimated previously from experiments and those obtained from a standard computational method based on a series of constrained tension simulations. We further validate our framework in a comparison with an existing polymer brush model and confirm the polymer brush model’s predicted linear relationship with proportionality coefficient of 24, using elastic parameters calculated from the simulation trajectories. The robustness of the results that emerge from the method allows us to revisit the origins of the bilayer mechanical (compressible) thickness and in particular its dependence on acyl-chain unsaturation and the presence of cholesterol.

59 BASIC BIOLOGICAL SCIENCES↗

WRATS Integrated Data Acquisition System

The Wing and Rotor Aeroelastic Test System (WRATS) data acquisition system (DAS) is a 64-channel data acquisition display and analysis system specifically designed for use with the WRATS 1/5-scale V-22 tiltrotor model of the Bell Osprey. It is the primary data acquisition system for experimental aeroelastic testing of the WRATS model for the purpose of characterizing the aeromechanical and aeroelastic stability of prototype tiltrotor configurations. The WRATS DAS was also used during aeroelastic testing of Bell Helicopter Textron s Quad-Tiltrotor (QTR) design concept, a test which received international attention. The LabVIEW-based design is portable and capable of powering and conditioning over 64 channels of dynamic data at sampling rates up to 1,000 Hz. The system includes a 60-second circular data archive, an integrated model swashplate excitation system, a moving block damping application for calculation of whirl flutter mode subcritical damping, a loads and safety monitor, a pilot-control console display, data analysis capabilities, and instrumentation calibration functions. Three networked computers running custom-designed LabVIEW software acquire data through National Instruments data acquisition hardware. The aeroelastic model (see figure) was tested with the DAS at two facilities at NASA Langley, the Transonic Dynamics Tunnel (TDT) and the Rotorcraft Hover Test Facility (RHTF). Because of the need for seamless transition between testing at these facilities, DAS is portable. The software is capable of harmonic analysis of periodic time history data, Fast Fourier Transform calculations, power spectral density calculations, and on-line calibration of test instrumentation. DAS has a circular buffer archive to ensure critical data is not lost in event of model failure/incident, as well as a sample-and-hold capability for phase-correct time history data.

Piatak, David J.↗

Adaptive Sampling for In Situ Cloud Probe (Final Report)

Clouds play a leading role in the Earth's global energy and solar radiation balance and hydrological cycle. Improving cloud models requires detailed information on the cloud microphysical properties, such as droplet size distribution and number density, liquid water content and cloud composition (droplets, ice particles), which can only be provided by aerial in situ measurements. However, for many atmospheric measurement instruments, the lack of flexibility in selecting the operational mode during operation can lead to uncertainties in sampling and measurement characteristics under continuously varying atmospheric conditions. This SBIR project is developing an advanced, compact optical imaging technology for in situ characterization of cloud hydrometeors. The development involves a deep modification of the existing Mesa Photonics’ Cloud Droplet Measurement System (CDMS) in order to implement real-time automatic adaptive sampling based on the acquired in situ data and environmental parameters. The new system, CDMS-2, implements two measurement modes: side-scatter imaging for smaller hydrometeors and direct bright-field-illumination imaging for larger hydrometeors in a significantly larger sample volume. The system measures the droplet size distribution (DSD) and number density with an added capability of discriminating between liquid water and ice hydrometeors (based on polarization-resolved side-scatter imaging). The instrument will implement automatic switching or alternating between the regular side-scatter imaging mode and sparse/large hydrometeor mode (based on the acquired data). Other adaptive sampling capabilities include variable sample volume and dynamic range (based on the measured DSD). The preferred deployment platforms are uncrewed aircraft systems (UAS) and tethered balloon/kite systems (TBS). The Phase I project achieved (or exceeded) the goals listed in the Work Plan. A CDMS-2 laboratory prototype implementing the polarization-resolved side-scatter imaging mode and direct bright-field-illumination imaging mode was designed and built. Additional capabilities included the variable illumination pulse energy and sample volume. The smallest detectable droplet diameter was improved to 3–4 μm (from the nominal 10 μm value specified for the original CDMS). Discrimination between water droplets and ice particles was experimentally demonstrated. The Phase I prototype was extensively tested and calibrated in the laboratory and also tested in the Pi Cloud Chamber at Michigan Technological University (MTU). The two intensive experimental campaigns at MTU provided unique opportunities of testing the CDMS-2 laboratory prototype under realistic warm and mixed-phase cloud conditions (stable for long periods of time), testing different sampling modes and intercomparing the CDMS-2 prototype to other co-located cloud characterization instruments. The Phase I project successfully demonstrated the feasibility of the proposed technology and identified the engineering challenges of designing a field deployable prototype instrument in Phase II. The Phase I study provides a solid basis for development, characterization and field-testing of the proposed advanced cloud probe with adaptive sampling in Phase II followed by commercialization of the technology in Phase III.

47 OTHER INSTRUMENTATION↗

SympNets: Intrinsic structure-preserving symplectic networks for identifying Hamiltonian systems

Here, we propose new symplectic networks (SympNets) for identifying Hamiltonian systems from data based on a composition of linear, activation and gradient modules. In particular, we define two classes of SympNets: the LA-SympNets composed of linear and activation modules, and the G-SympNets composed of gradient modules. Correspondingly, we prove two new universal approximation theorems that demonstrate that SympNets can approximate arbitrary symplectic maps based on appropriate activation functions. We then perform several experiments including the pendulum, double pendulum and three-body problems to investigate the expressivity and the generalization ability of SympNets. The simulation results show that even very small size SympNets can generalize well, and are able to handle both separable and non-separable Hamiltonian systems with data points resulting from short or long time steps. In all the test cases, SympNets outperform the baseline models, and are much faster in training and prediction. We also develop an extended version of SympNets to learn the dynamics from irregularly sampled data. This extended version of SympNets can be thought of as a universal model representing the solution to an arbitrary Hamiltonian system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Flight dynamics system software development environment (FDS/SDE) tutorial

A sample development scenario using the Flight Dynamics System Software Development Environment (FDS/SDE) is presented. The SDE uses a menu-driven, fill-in-the-blanks format that provides online help at all steps, thus eliminating lengthy training and allowing immediate use of this new software development tool.

Buell, John↗

Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers

Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode structure and functionality by having various side chains. Through molecular dynamics (MD) simulations, the triazine polymers have been shown to form particular sequential stacks, have stable backbone-backbone interactions through hydrogen bonding and π–π interactions, and conserve their cis/trans conformations throughout the simulation. However, we do not know the effects of having different side chains and backbone structures on the entire conformation and whether the cis or trans conformation is more stable for the triazine polymers. For this reason, we investigate the role of non-covalent interactions for different side chains and backbone structures on the conformation and assembly of triazine polymers in MD simulations. Since there is a high energy barrier associated with the cis-trans isomerization, we use replica exchange molecular dynamics (REMD) to sample various conformations of triazine hexamers. To obtain rates and intermediate conformations, we use the recently developed concurrent adaptive sampling (CAS) algorithm for dimers of triazine trimers. Here, we found that the hydrogen bonding ability of the backbone structure is critical for the triazine polymers to self-assemble into nanorod-like structures, rather than that of the side chains, which can help researchers design more robust materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analytic rate theory of polariton relaxation that explains long polariton lifetime

Hybridization of a molecular exciton with a quantized photon creates a polariton. Despite extensive experimental investigations, the apparent lifetime of the exciton–polariton is not well-understood. For this work, we examined the steady-state population dynamics for a Holstein–Tavis–Cumming Hamiltonian to illuminate the long-term polaritonic dynamics and lifetime of the exciton–polariton in an optical cavity. For a realistic description of polariton relaxation, cavity loss and various exciton decay channels are included in the model. We found that in the presence of weak but finite exciton loss, the apparent lifetime of the lower polariton coincides with the out-of-cavity exciton lifetime and is independent of cavity-matter detuning. This is a simple explanation for the experimentally observed lifetimes for exciton polaritons and theoretically justifies the dark state reservoir hypothesis. Furthermore, if the upper polariton is initially populated, the system reaches the steady state very quickly, leading to single-exponential polariton relaxation. Starting from the lower polariton leads to a longer pre-steady-state time period, leading to double-exponential relaxation. Finally, we considered the effect of site orientational disorders and the exciton frequency disorderers. Under the collective limit, the effects of this disorder can be included in Fermi’s golden rule population dynamics without explicit sampling. For the exciton energy disorders, numerical calculations are needed. Our theoretical framework is applicable to interpret exciton–polariton experiments, especially related to the measured apparent lifetime of polaritons.

Chemical dynamics↗

Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16

ABSTRACT In the CASP16 experiment, our team employed hybrid computational strategies to predict both protein–protein and protein–ligand complex structures. For protein–protein docking, we combined physics‐based sampling—using ClusPro FFT docking and molecular dynamics—with AlphaFold (AF)‐based sampling, followed by AF‐based refinement. Our method produced numerous high‐accuracy complex models, including cases where AF alone failed, underscoring the critical role of physics‐based sampling alongside deep learning‐based refinement. For protein–ligand docking, we integrated the ClusPro LigTBM template‐based approach with a machine learning‐based confidence model for rescoring. The method preserves conserved interaction fragments derived from homologous complexes, followed by local resampling using physics‐based sampling and a diffusion model. Our template‐based strategy achieved a mean lDDT‐PLI of 0.69 across 233 targets, which was highly competitive. These results demonstrate that combining physics‐based modeling with AI‐driven refinement can significantly enhance the accuracy of both protein–protein and protein–ligand structure predictions.

Ashizawa, Ryota [Department of Applied Mathematics↗

Engine identification for adaptive control

An attempt to obtain a dynamic model for a turbofan gas turbine engine for the purpose of adaptive control is described. The requirements for adaptive control indicate that a dynamic model should be identified from data sampled during engine operation. The dynamic model identified was of the form of linear differential equations with time varying coefficients. A turbine engine is, however, a highly nonlinear system, so the identified model would be valid only over a small area near the operating point, thus requiring frequent updating of the coefficients in the model. Therefore it is necessary that the identifier use only recent information to perform its function. The identifier selected minimized the square of the equation errors. Known linear systems were used to test the characteristics of the identifier. It was found that the performance was dependent on the number of data points used in the computations and upon the time interval over which the data points were obtained. Preliminary results using an engine deck for the quiet, clean, shorthaul experimental engine indicate that the identified model predicts the engine motion well when there is sufficient dynamic information, that is when the engine is in transient operation.

Leonard, R. G.↗